There are similarities such as city shape, being the biggest most important city on its continent, troops on Griffin back, politics and trade dominated by a mix of Guilds and Noble Houses, a sizable surrounding territory around the city.
But Waterdeep is far, far more gonzo in some many ways, from raw population size (even Baldur's Gate has alot more population then Greyhawk in the city proper), to magic, wealth, infrastructure, and species diversity.
Waterdeep has giant animated statues, Undermountain (its megadungeon has its dungeons and town), the Temple of Mystra and the Seldarine (and a host of others, not small temples either), A MYTHAL protecting it from Dragon attacks, enough wealth and magic that it magically transports alot of its building materials, it's Open Lord Laeral Silverhand is a challenge rating 17 vs 12 for Mordy, and the current Blackstaff I read on a wiki challenge 13, the roads going into and out of it in its territories are paved, not girl. It has Nimblewrights and goods from Lantan and Baldur's Gate and it's own temple of Gond. It has public transportation the Drays, teleportation circles, portals to other planes, powerful allies, Spelljammer port of sorts, it was so rich until rescently it didn't even bother with taxes outside of emergencies.
Waterdeep is also on the Ocean so it trades with other continents and nations, as well as tapping into the vast resources of the Ocean (fish, pearls, etc..., major roadways to the North, South, and East towards the Sea of Fallen Stars, connections to the Underdark, major industry.
So I think in original conception both had the same basic inspiration, but overtime Waterdeep just kept getting juiced up and juiced up.
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